“Candidatus Thermonerobacter thiotrophicus,” A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities

Flavin-Based Electron Bifurcation, A New Mechanism of Biological Energy Coupling

(2018) Wolfgang Buckel et al.   CHEMICAL REVIEWS

Peatland Acidobacteria with a dissimilatory sulfur metabolism

(2018) Bela Hausmann et al.   ISME Journal

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

(2018) Karthik Anantharaman et al.   ISME Journal

Nitrogen Fixation in Thermophilic Chemosynthetic Microbial Communities Depending on Hydrogen, Sulfate, and Carbon Dioxide

(2018) Arisa Nishihara et al.   MICROBES AND ENVIRONMENTS

Long-Term Cultivation and Metagenomics Reveal Ecophysiology of Previously Uncultivated Thermophiles Involved in Biogeochemical Nitrogen Cycle

(2018) Shingo Kato et al.   MICROBES AND ENVIRONMENTS

Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD+ (Rnf) as Electron Acceptors: A Historical Review

(2018) Wolfgang Buckel et al.   Frontiers in Microbiology

Stable Isotope Probing for Microbial Iron Reduction in Chocolate Pots Hot Spring, Yellowstone National Park

(2018) Nathaniel W. Fortney et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Growth of an anaerobic sulfate-reducing bacterium sustained by oxygen respiratory energy conservation after O2 -driven experimental evolution

(2018) Marine Schoeffler et al.   ENVIRONMENTAL MICROBIOLOGY

Characterization of the sulfur-formation (suf) genes in Synechocystis sp. PCC 6803 under photoautotrophic and heterotrophic growth conditions

(2017) Sha-Sha Zang et al.   PLANTA

Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium Desulfurivibrio alkaliphilus by Sulfide Oxidation with Nitrate

(2017) Casper Thorup et al.   mBio

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses

(2017) Vera Thiel et al.   Frontiers in Microbiology

Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics

(2016) Claus Pelikan et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial Fe(III) oxide reduction potential in Chocolate Pots hot spring, Yellowstone National Park

(2016) N. W. Fortney et al.   Geobiology

Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly

(2016) Tomàs Llorens–Marès et al.   ISME Journal

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

(2016) Daan R. Speth et al.   Nature Communications

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing

(2016) Vera Thiel et al.   Frontiers in Microbiology

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics

(2015) Rose S. Kantor et al.   ENVIRONMENTAL MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Chloracidobacterium thermophilum gen. nov., sp. nov.: an anoxygenic microaerophilic chlorophotoheterotrophic acidobacterium

(2015) M. Tank et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes

(2015) Aharon Oren et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage

(2015) Jennifer Hiras et al.   ISME Journal

A protein trisulfide couples dissimilatory sulfate reduction to energy conservation

(2015) A. A. Santos et al.   SCIENCE

Nutrient requirements and growth physiology of the photoheterotrophic Acidobacterium, Chloracidobacterium thermophilum

(2015) Marcus Tank et al.   Frontiers in Microbiology

A Comparative Quantitative Proteomic Study Identifies New Proteins Relevant for Sulfur Oxidation in the Purple Sulfur Bacterium Allochromatium vinosum

(2014) Thomas Weissgerber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases

(2014) Albert Leopold Müller et al.   ISME Journal

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

(2013) Sergey I Nikolenko et al.   BMC GENOMICS

EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes

(2013) Tanja Magoc et al.   Evolutionary Bioinformatics

AmphoraNet: The webserver implementation of the AMPHORA2 metagenomic workflow suite

(2013) Csaba Kerepesi et al.   GENE

Temporal metatranscriptomic patterning in phototrophic Chloroflexi inhabiting a microbial mat in a geothermal spring

(2013) Christian G Klatt et al.   ISME Journal

A Phylum-Level Bacterial Phylogenetic Marker Database

(2013) Zhang Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

IMG/M 4 version of the integrated metagenome comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Genomic Analysis of Melioribacter roseus, Facultatively Anaerobic Organotrophic Bacterium Representing a Novel Deep Lineage within Bacteriodetes/Chlorobi Group

(2013) Vitaly V. Kadnikov et al.   PLoS One

Unifying concepts in anaerobic respiration: Insights from dissimilatory sulfur metabolism

(2012) Fabian Grein et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Characterization ofMelioribacter roseusgen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the classIgnavibacteria, and a proposal of a novel bacterial phylumIgnavibacteriae

(2012) Olga A. Podosokorskaya et al.   ENVIRONMENTAL MICROBIOLOGY

‘Candidatus Thermochlorobacter aerophilum:’ an aerobic chlorophotoheterotrophic member of the phylum Chlorobi defined by metagenomics and metatranscriptomics

(2012) Zhenfeng Liu et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem

(2012) Hideto Takami et al.   PLoS One

Sulfate-reducing microorganisms in wetlands – fameless actors in carbon cycling and climate change

(2012) Michael Pester   Frontiers in Microbiology

Complete Genome of Ignavibacterium album, a Metabolically Versatile, Flagellated, Facultative Anaerobe from the Phylum Chlorobi

(2012) Zhenfeng Liu et al.   Frontiers in Microbiology

Genomics of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia sp. Strain MED134

(2011) José M. González et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evidence for Aquaporin-mediated Water Transport in Nematocytes of the Jellyfish Pelagia noctiluca

(2011) Angela Marino et al.   CELLULAR PHYSIOLOGY AND BIOCHEMISTRY

Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

(2011) Christian G Klatt et al.   ISME Journal

Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat

(2011) Zhenfeng Liu et al.   ISME Journal

Sulfur globule oxidation in green sulfur bacteria is dependent on the dissimilatory sulfite reductase system

(2011) C. Holkenbrink et al.   MICROBIOLOGY-SGM

Microfossils of sulphur-metabolizing cells in 3.4-billion-year-old rocks of Western Australia

(2011) David Wacey et al.   Nature Geoscience

Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life?

(2010) Georg Fuchs   Annual Review of Microbiology

Diversity of Dissimilatory Sulfite Reductase Genes (dsrAB) in a Salt Marsh Impacted by Long-Term Acid Mine Drainage

(2010) J. W. Moreau et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Novel groups of Gammaproteobacteria catalyse sulfur oxidation and carbon fixation in a coastal, intertidal sediment

(2010) Sabine Lenk et al.   ENVIRONMENTAL MICROBIOLOGY

A ‘rare biosphere’ microorganism contributes to sulfate reduction in a peatland

(2010) Michael Pester et al.   ISME Journal

Comprehensive Detection of Phototrophic Sulfur Bacteria Using PCR Primers That Target Reverse Dissimilatory Sulfite Reductase Gene

(2010) Yumi Mori et al.   MICROBES AND ENVIRONMENTS

Hydrogen peroxide inactivates the Escherichia coli Isc iron-sulphur assembly system, and OxyR induces the Suf system to compensate

(2010) Soojin Jang et al.   MOLECULAR MICROBIOLOGY

MICROBIAL BIOSIGNATURES IN IRON-MINERALIZED PHOTOTROPHIC MATS AT CHOCOLATE POTS HOT SPRINGS, YELLOWSTONE NATIONAL PARK, UNITED STATES

(2010) M. N. PARENTEAU et al.   PALAIOS

A Cryptic Sulfur Cycle in Oxygen-Minimum-Zone Waters off the Chilean Coast

(2010) D. E. Canfield et al.   SCIENCE

Multiple antioxidant proteins protect Chlorobaculum tepidum against oxygen and reactive oxygen species

(2009) Hui Li et al.   ARCHIVES OF MICROBIOLOGY

Ignavibacterium album gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from microbial mats at a terrestrial hot spring and proposal of Ignavibacteria classis nov., for a novel lineage at the periphery of green sulfur bacteria

(2009) T. Iino et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The Iron-Hydrogenase of Thermotoga maritima Utilizes Ferredoxin and NADH Synergistically: a New Perspective on Anaerobic Hydrogen Production

(2009) G. J. Schut et al.   JOURNAL OF BACTERIOLOGY

The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes

(2009) Konstantinos Mavromatis et al.   Standards in Genomic Sciences

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

Phyutility: a phyloinformatics tool for trees, alignments and molecular data

(2008) S. A. Smith et al.   BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes

(2008) Alexander Loy et al.   ENVIRONMENTAL MICROBIOLOGY

Fe-S Cluster Assembly Pathways in Bacteria

(2008) C. Ayala-Castro et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS